if($sequence[1] =~ m/^(.*)$reg(.*)$/i){
          $aligned[$posCount][0] = $1;
          $aligned[$posCount][1] = $2;
          $aligned[$posCount][2] = $3;
}

##</code><code>##

if($sequence[1] =~ m/^(.*)$reg(.*)$/i){
         for(my $x = 0; $x < $numInsertionDeletes; $x++){
               $aligned[$posCount][$x] = ????????;
         }
      }